3ZDD | pdb_00003zdd

Structure of E. coli ExoIX in complex with the palindromic 5ov6 oligonucleotide and potassium

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	APG6	e3zddA1	A: alpha bundles	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02739	5'-3' exonuclease, N-terminal resolvase-like domain (5_3_exonuc_N)	5'-3' exonuclease, N-terminal resolvase-like domain		Domain
A	PF01367	5'-3' exonuclease, C-terminal SAM fold (5_3_exonuc)	5'-3' exonuclease, C-terminal SAM fold		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	5OV6 DNA	-	-	-
A	PROTEIN XNI	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding potassium ion binding alkali metal ion binding 5'-flap endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding potassium ion binding alkali metal ion binding 5'-flap endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity flap endonuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity 5'-3' exonuclease activity exonuclease activity	DNA-templated DNA replication lagging strand elongation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication DNA replication, Okazaki fragment processing metabolic process cellular process DNA strand elongation involved in DNA replication macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002421	5'-3' exonuclease	Domain
A	IPR020045	DNA polymerase I-like, H3TH domain	Domain
A	IPR038969	Flap endonuclease	Family
A	IPR029060	PIN-like domain superfamily	Homologous Superfamily
A	IPR036279	5'-3' exonuclease, C-terminal domain superfamily	Homologous Superfamily
A	IPR008918	Helix-hairpin-helix motif, class 2	Conserved Site
A	IPR020046	5'-3' exonuclease, alpha-helical arch, N-terminal	Domain
A	IPR022895	Flap endonuclease Xni	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.